In chronic myeloid leukemia patients on second-line tyrosine kinase inhibitor therapy, deep sequencing of BCR-ABL1 at the time of warning may allow sensitive detection of emerging drug-resistant mutants

Abstract

BackgroundImatinib-resistant chronic myeloid leukemia (CML) patients receiving second-line tyrosine kinase inhibitor (TKI) therapy with dasatinib or nilotinib have a higher risk of disease relapse and progression and not infrequently BCR-ABL1 kinase domain (KD) mutations are implicated in therapeutic failure. In this setting, earlier detection of emerging BCR-ABL1 KD mutations would offer greater chances of efficacy for subsequent salvage therapy and limit the biological consequences of full BCR-ABL1 kinase reactivation. Taking advantage of an already set up and validated next-generation deep amplicon sequencing (DS) assay, we aimed to assess whether DS may allow a larger window of detection of emerging BCR-ABL1 KD mutants predicting for an impending relapse.Methodsa total of 125 longitudinal samples from 51 CML patients who had acquired dasatinib- or nilotinib-resistant mutations during second-line therapy were analyzed by DS from the time of failure and mutation detection by conventional sequencing backwards. BCR-ABL1/ABL1%IS transcript levels were used to define whether the patient had ‘optimal response’, ‘warning’ or ‘failure’ at the time of first mutation detection by DS.ResultsDS was able to backtrack dasatinib- or nilotinib-resistant mutations to the previous sample(s) in 23/51 (45 %) pts. Median mutation burden at the time of first detection by DS was 5.5 % (range, 1.5–17.5 %); median interval between detection by DS and detection by conventional sequencing was 3 months (range, 1–9 months). In 5 cases, the mutations were detectable at baseline. In the remaining cases, response level at the time mutations were first detected by DS could be defined as ‘Warning’ (according to the 2013 ELN definitions of response to 2nd-line therapy) in 13 cases, as ‘Optimal response’ in one case, as ‘Failure’ in 4 cases. No dasatinib- or nilotinib-resistant mutations were detected by DS in 15 randomly selected patients with ‘warning’ at various timepoints, that later turned into optimal responders with no treatment changes.ConclusionsDS enables a larger window of detection of emerging BCR-ABL1 KD mutations predicting for an impending relapse. A ‘Warning’ response may represent a rational trigger, besides ‘Failure’, for DS-based mutation screening in CML patients undergoing second-line TKI therapy.

Incidence and outcome of BCR‐ABL mutated chronic myeloid leukemia patients who failed to tyrosine kinase inhibitors

“…These results suggest that earlier detection of BCR‐ABL KD mutation together with accessibility to 2‐3GTKI and therapeutic change based on preclinical and clinical available data on TKI sensitivity for a given mutation have significantly improved the outcome of mutated patients, as long as the disease remains in CP at the time of mutation identification. Previous published studies have demonstrated that, using more sensitive techniques such as next generation sequencing (NGS), BCR‐ABL KD mutations can be detected earlier and at a very low level . Whether early mutation detection using NGS together with the switch to other currently available TKIs will prevent progression of the disease in mutated patients is currently under investigation.…”

Chronic Myeloid Leukemia, Version 2.2021, NCCN Clinical Practice Guidelines in Oncology

“…Next generation sequencing (NGS) allows for the detection of low-level BCR-ABL1 kinase domain mutations as well as resistance mutations in genes other than BCR-ABL1 that may confer resistance to TKIs or portend disease progression. [62][63][64][65] In a recent prospective, multicenter study (NEXT-in-CML) that assessed the feasibility of NGS in detection of low-level mutations in 236 consecutive patients with CML and inadequate response to TKI therapy, NGS was more effective than conventional Sanger sequencing in the detection of low-level mutations. 65 Prospective monitoring of mutation kinetics demonstrated that TKI-resistant low-level mutations are invariably selected if the patients are not switched to another TKI or if they are switched to an inappropriate TKI or TKI dose.…”

The Polycomb BMI1 Protein Is Co-expressed With CD26+ in Leukemic Stem Cells of Chronic Myeloid Leukemia

“…There are several mechanisms leading to the resistance, which haven't been well identified yet: in some cases, ABL1 mutations impair the insertion of the TKI into the ATP-binding pocket of the fusion protein (4), but in the majority the activation of alternative pro-proliferating pathways, such as JAK-STAT, B-catenin/Wnt, Hedgehog , or the abnormal epigenetic control, can occur (5, 6).…”